Dynamic deformylation of 5-formylcytosine and decarboxylation of 5-carboxylcytosine during differentiation of mouse embryonic stem cells into mouse neurons

Abstract

Regulation of cell fate requires the establishment and erasure of 5-methylcytosine (5mC) in genomic DNA. The formation of 5mC is achieved by DNA cytosine methyltransferases (DNMTs), whereas the removal of 5mC can be accomplished by various pathways. Aside from ten-eleven translocation (TET)-mediated oxidation of 5mC followed by thymine DNA glycosylase (TDG)-initiated base excision repair (BER), the direct deformylation of 5-formylcytosine (5fC) and decarboxylation of 5-carboxylcytosine (5caC) have also been discovered as the novel DNA demethylation pathways. Although these novel demethylation pathways have been identified in stem cells and somatic cells, their precise roles in regulating cell fate remain unclear. Here, we differentiate mouse embryonic stem cells (mESCs) into mouse embryoid bodies (mEBs), followed by further differentiation into mouse neural stem cells (mNSCs) and finally into mouse neurons (mNeurons). During this sequential differentiation process, we employ probe molecules, namely 2′-fluorinated 5-formylcytidine (F-5fC) and 2′-fluorinated 5-carboxyldeoxycytidine (F-5caC), for metabolic labeling. The results of mass spectrometry (MS) analysis demonstrate the deformylation and decarboxylation activities are progressively decreased and increased respectively during differentiation process, and this opposite demethylation tendency is not associated with DNMTs and TETs.